Merge branch 'develop' into feature/tier2-testing

parm/soca/letkf/letkf.yaml.j2

@@ -11,8 +11,8 @@ background:
   members from template:
     template:
       date: '{{ WINDOW_MIDDLE | to_isotime }}'
-      ocn_filename: "{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc"
-      ice_filename: "{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc"
+      ocn_filename: "{{ RUN }}.ocean.t{{ gcyc }}z.inst.f006.nc"
+      ice_filename: "{{ RUN }}.ice.t{{ gcyc }}z.inst.f006.nc"
       read_from_file: 1
       basename: ./ens/mem%mem%
       state variables: [socn, tocn, ssh, uocn, vocn, cicen]

parm/soca/letkf/letkf_stage.yaml.j2

@@ -1,49 +1,11 @@
 ######################################
-# set some variables
-######################################
-{% set gPDY = previous_cycle | to_YMD %}
-{% set gcyc = previous_cycle | strftime("%H") %}
-{% set PDY = current_cycle | to_YMD %}
-{% set cyc = current_cycle | strftime("%H") %}
-######################################
 # create working directories
 ######################################
 mkdir:
 - "{{ DATA }}/Data"
 - "{{ DATA }}/obs"
-- "{{ DATA }}/INPUT"
-{% for mem in range(1, NMEM_ENS + 1) %}
-- "{{ DATA }}/ens/mem{{ '%03d' % mem }}"
-{% endfor %}
 copy:
 ######################################
 # copy mom input template 
 ######################################
 - ["{{ PARMgfs }}/gdas/soca/fms/input.nml", "{{ DATA }}/mom_input.nml.tmpl"]
-######################################
-# copy ensemble background files
-######################################
-{% for mem in range(1, NMEM_ENS + 1) %}
-# define variables
-# Declare a dict of search and replace terms to GDUMP on each template
-{% set tmpl_dict = {'ROTDIR':ROTDIR,
-                    'RUN': GDUMP_ENS,
-                    'YMD':gPDY,
-                    'HH':gcyc,
-                    'MEMDIR':"mem" + '%03d' % mem} %}
-
-# Replace template variables with tmpl_dict, one key at a time
-# This must be done in a namespace to overcome jinja scoping
-#  Variables set inside of a for loop are lost at the end of the loop
-#  unless they are part of a namespace
-{% set com_prev_ocn = namespace(COMIN_OCEAN_HISTORY_MEM = COM_OCEAN_HISTORY_TMPL) %}
-{% set com_prev_ice = namespace(COMIN_ICE_HISTORY_MEM = COM_ICE_HISTORY_TMPL) %}
-{% for key in tmpl_dict.keys() %}
-{% set search_term = '${' + key + '}' %}
-{% set replace_term = tmpl_dict[key] %}
-{% set com_prev_ocn.COMIN_OCEAN_HISTORY_MEM = com_prev_ocn.COMIN_OCEAN_HISTORY_MEM.replace(search_term, replace_term) %}
-{% set com_prev_ice.COMIN_ICE_HISTORY_MEM = com_prev_ice.COMIN_ICE_HISTORY_MEM.replace(search_term, replace_term) %}
-{% endfor %}
-- ["{{ com_prev_ocn.COMIN_OCEAN_HISTORY_MEM }}/{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc", "{{ DATA }}/ens/mem{{ '%03d' % mem }}/{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc"]
-- ["{{ com_prev_ice.COMIN_ICE_HISTORY_MEM }}/{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc", "{{ DATA }}/ens/mem{{ '%03d' % mem }}/{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc"]
-{% endfor %}

parm/soca/soca_ens_bkg_stage.yaml.j2

@@ -0,0 +1,40 @@
+######################################
+# set some variables
+######################################
+{% set gPDY = previous_cycle | to_YMD %}
+{% set gcyc = previous_cycle | strftime("%H") %}
+######################################
+# create ens bkg directories
+######################################
+mkdir:
+{% for mem in range(1, NMEM_ENS + 1) %}
+   - "{{ DATA }}/ens/mem{{ '%03d' % mem }}"
+{% endfor %}
+######################################
+# copy ensemble background files
+######################################
+copy:
+{% for mem in range(1, NMEM_ENS + 1) %}
+   # define variables
+   # Declare a dict of search and replace terms to GDUMP on each template
+   {% set tmpl_dict = {'ROTDIR':ROTDIR,
+                       'RUN': RUN,
+                       'YMD':gPDY,
+                       'HH':gcyc,
+                       'MEMDIR':"mem" + '%03d' % mem} %}
+
+   # Replace template variables with tmpl_dict, one key at a time
+   # This must be done in a namespace to overcome jinja scoping
+   #  Variables set inside of a for loop are lost at the end of the loop
+   #  unless they are part of a namespace
+   {% set com_prev_ocn = namespace(COMIN_OCEAN_HISTORY_MEM = COM_OCEAN_HISTORY_TMPL) %}
+   {% set com_prev_ice = namespace(COMIN_ICE_HISTORY_MEM = COM_ICE_HISTORY_TMPL) %}
+   {% for key in tmpl_dict.keys() %}
+      {% set search_term = '${' + key + '}' %}
+      {% set replace_term = tmpl_dict[key] %}
+      {% set com_prev_ocn.COMIN_OCEAN_HISTORY_MEM = com_prev_ocn.COMIN_OCEAN_HISTORY_MEM.replace(search_term, replace_term) %}
+      {% set com_prev_ice.COMIN_ICE_HISTORY_MEM = com_prev_ice.COMIN_ICE_HISTORY_MEM.replace(search_term, replace_term) %}
+   {% endfor %}
+   - ["{{ com_prev_ocn.COMIN_OCEAN_HISTORY_MEM }}/{{ RUN }}.ocean.t{{ gcyc }}z.inst.f006.nc", "{{ DATA }}/ens/mem{{ '%03d' % mem }}/{{ RUN }}.ocean.t{{ gcyc }}z.inst.f006.nc"]
+   - ["{{ com_prev_ice.COMIN_ICE_HISTORY_MEM }}/{{ RUN }}.ice.t{{ gcyc }}z.inst.f006.nc", "{{ DATA }}/ens/mem{{ '%03d' % mem }}/{{ RUN }}.ice.t{{ gcyc }}z.inst.f006.nc"]
+{% endfor %}

parm/soca/letkf/soca_fix_stage.yaml.j2 → parm/soca/soca_fix_stage.yaml.j2

@@ -1,3 +1,6 @@
+# TODO(AFE): make resolution dependent
+mkdir:
+- "{{ DATA }}/INPUT"
 ######################################
 # fix files to copy
 ######################################

test/CMakeLists.txt

@@ -126,13 +126,14 @@ add_test(NAME test_gdasapp_jedi_increment_to_fv3
          WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/)
 
 # high level tests that require the global-workflow
-if (WORKFLOW_TESTS)
-
-  # test for creating an experiment directory within the global-workflow
-  add_test(NAME test_gdasapp_setup_cycled_exp
-           COMMAND ${PROJECT_SOURCE_DIR}/test/setup_workflow_exp.sh ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
-           WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/testrun)
-endif()
+# TODO(AFE) see GDASApp issue #1213
+#if (WORKFLOW_TESTS)
+#
+#  # test for creating an experiment directory within the global-workflow
+#  add_test(NAME test_gdasapp_setup_cycled_exp
+#           COMMAND ${PROJECT_SOURCE_DIR}/test/setup_workflow_exp.sh ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
+#           WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/testrun)
+#endif()
 
 if (${BUILD_GDASBUNDLE})
   add_subdirectory(fv3jedi)   # fv3jedi tests